Package: decontX 1.11.2

Joshua Campbell

decontX: Decontamination of single cell genomics data

This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2024), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.

Authors:Yuan Yin [aut], Masanao Yajima [aut], Joshua Campbell [aut, cre]

decontX_1.11.2.tar.gz
decontX_1.11.2.zip(r-4.7-x86_64)decontX_1.11.2.zip(r-4.7-arm64)decontX_1.11.2.zip(r-4.6-x86_64)decontX_1.11.2.zip(r-4.6-arm64)decontX_1.11.2.zip(r-4.5-x86_64)
decontX_1.11.2.tgz(r-4.6-x86_64)decontX_1.11.2.tgz(r-4.6-arm64)decontX_1.11.2.tgz(r-4.5-x86_64)decontX_1.11.2.tgz(r-4.5-arm64)
decontX_1.11.2.tar.gz(r-4.7-arm64)decontX_1.11.2.tar.gz(r-4.7-x86_64)decontX_1.11.2.tar.gz(r-4.6-arm64)decontX_1.11.2.tar.gz(r-4.6-x86_64)
decontX_1.11.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
decontX/json (API)

# Install 'decontX' in R:
install.packages('decontX', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/campbio/decontx/issues

Uses libs:
  • onetbb– Parallelism library for C++
  • c++– GNU Standard C++ Library v3

On BioConductor:decontX-1.11.2(bioc 3.24)decontX-1.10.0(bioc 3.23)

singlecellbayesiangeneexpressionrnaseqproteomicspreprocessingnormalizationqualitycontrolonetbbcpp

7.49 score 70 stars 1 packages 113 scripts 1.3k downloads 11 exports 93 dependencies

Last updated from:3d7a8aa126. Checks:1 NOTE, 11 WARNING, 3 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE278
linux-devel-arm64WARNING391
linux-devel-x86_64WARNING457
source / vignettesERROR489
linux-release-arm64WARNING404
linux-release-x86_64WARNING568
macos-release-arm64WARNING404
macos-release-x86_64WARNING660
macos-oldrel-arm64WARNING503
macos-oldrel-x86_64WARNING748
windows-devel-arm64ERROR574
windows-devel-x86_64WARNING2453
windows-release-arm64ERROR506
windows-release-x86_64WARNING2382
windows-oldrel-x86_64WARNING2374
wasm-releaseOK193

Exports:decontProdecontXdecontXcountsdecontXcounts<-plotBoxByClusterplotDecontXContaminationplotDecontXMarkerExpressionplotDecontXMarkerPercentageplotDensityretrieveFeatureIndexsimulateContamination

Dependencies:abindassortheadbackportsbeachmatBHBiobaseBiocGenericsbiocmakeBiocNeighborscallrcheckmateclicodetoolscombinatcpp11dbscanDelayedArraydescdigestdir.expirydistributionaldotCall64farverfilelockfuturefuture.applygenericsGenomicRangesggplot2globalsgluegridExtragtableinlineIRangesisobandlabelinglatticelifecyclelistenvloomagrittrMatrixMatrixGenericsmatrixStatsMCMCprecisionnumDerivotelparallellypatchworkpillarpkgbuildpkgconfigplyrposteriorprocessxprogressrpsQuickJSRR6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRcppProgressreshape2RigraphlibrlangrstanrstantoolsS4ArraysS4VectorsS7scalesscrapperSeqinfoSeuratObjectSingleCellExperimentspspamSparseArrayStanHeadersstringistringrSummarizedExperimenttensorAtibbleutf8vctrsviridisLitewithrXVector

Readme and manuals

Help Manual

Help pageTopics
The 'decontX' package.decontX-package
Call Stan variational bayes for inference.call_stan_vb
Process Stan output..process_stan_vb_out
Decontaminate using decontProdecontPro decontPro,ANY-method decontPro,Seurat-method decontPro,SingleCellExperiment-method
Contamination estimation with decontXdecontX decontX,ANY-method decontX,SingleCellExperiment-method
Get or set decontaminated counts matrixdecontXcounts decontXcounts,SingleCellExperiment-method decontXcounts<- decontXcounts<-,SingleCellExperiment-method
Fast normalization for numeric matrixfastNormProp
Fast normalization for numeric matrixfastNormPropLog
Fast normalization for numeric matrixfastNormPropSqrt
get row and column indices of none zero elements in the matrixnonzero
Boxplot of features grouped by cell typeplotBoxByCluster
Plots contamination on UMAP coordinatesplotDecontXContamination
Plots expression of marker genes before and after decontaminationplotDecontXMarkerExpression
Plots percentage of cells cell types expressing markersplotDecontXMarkerPercentage
Density of each ADT, raw counts overlapped with decontaminated countsplotDensity
Retrieve row index for a set of featuresretrieveFeatureIndex
Simulate contaminated count matrixsimulateContamination